Sebastes genomic islands of divergence

Depth separation is a proposed driver of speciation in marine fishes, with
marine rockfish (genus Sebastes) providing a potentially
informative study system. Sebastes rockfishes are
commercially and ecologically important. This genus encompasses more than
one hundred species and the ecological and morphological variance between
these species provides opportunity for identifying speciation-driving
adaptations, particularly along a depth gradient. A reduced-representation
sequencing method (ddRADseq) was used to compare 95 individuals
encompassing six Sebastes species. In this study, we
sought to identify regions of divergence between species that were
indicative of divergent adaptation and reproductive barriers leading to
speciation. A pairwise comparison of S.
chrysomelas (black-and-yellow rockfish) and S.
carnatus (gopher rockfish) FST values revealed
three major regions of elevated genomic divergence, two of which were also
present in the S. miniatus (vermilion rockfish)
and S. crocotulus (sunset rockfish) comparison. Thses
corresponded with regions of both elevated DXY values
and reduced nucleotide diversity in two cases, suggesting a
speciation-with-gene-flow evolutionary model followed by post-speciation
selective sweeps within each species. Limited whole genome re-sequencing
was also performed to identify mutations with predicted effects
between S. chrysomelas and S. carnatus. Within
these islands, we identified important SNPs in genes involved in immune
function and vision. This supports the concept of depth-driven speciation,
as these are adaptive vectors noted in other organisms. Additionally,
changes to genes involved in pigment expression and mate recognition shed
light on how S. chrysomelas and S.
carnatus may have become reproductively isolated.